Molecular Devices GenePix 4000B User manual

Brand: Molecular Devices

Model: GenePix 4000B

Type: User manual

GenePix® 4000B Microarray Scanner

User Guide

5000450 D

October 2010

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This document is provided to customers who have purchased Molecular Devices, Inc.

(“Molecular Devices”) equipment, software, reagents, and consumables to use in the

operation of such Molecular Devices equipment, software, reagents, and

consumables. This document is copyright protected and any reproduction of this

document, in whole or any part, is strictly prohibited, except as Molecular Devices

may authorize in writing.

Software that may be described in this document is furnished under a license

agreement. It is against the law to copy, modify, or distribute the software on any

medium, except as specifically allowed in the license agreement. Furthermore, the

license agreement may prohibit the software from being disassembled, reverse

engineered, or decompiled for any purpose.

Portions of this document may make reference to other manufacturers and/or their

products, which may contain parts whose names are registered as trademarks and/or

function as trademarks of their respective owners. Any such usage is intended only

to designate those manufacturers' products as supplied by Molecular Devices for

incorporation into its equipment and does not imply any right and/or license to use

or permit others to use such manufacturers' and/or their product names as

trademarks.

Molecular Devices makes no warranties or representations as to the fitness of this

equipment for any particular purpose and assumes no responsibility or contingent

liability, including indirect or consequential damages, for any use to which the

purchaser may put the equipment described herein, or for any adverse circumstances

arising therefrom.

For research use only. Not for use in diagnostic procedures.

Product manufactured by Molecular Devices, Inc.

1311 Orleans Drive, Sunnyvale, California, United States of America 94089.

Molecular Devices, Inc. is ISO 9001 registered.

Printed in the USA.

The trademarks mentioned herein are the property of Molecular Devices, Inc. or their

respective owners. These trademarks may not be used in any type of promotion or

advertising without the prior written permission of Molecular Devices, Inc.

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GenePix 4000B Microarray Scanner User Guide

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Licensing Notice

Molecular Devices is not licensed under any patents owned by Oxford Gene Technology

Limited (“OGT”), covering oligonucleotide arrays and methods of using them to analyze

polynucleotides. The purchase of Molecular Devices products does not convey any license

under any of OGT’s patent rights, including any right to make or use oligonucleotide

arrays under OGT’s patents.

Customers may use Molecular Devices products to analyze oligonucleotide arrays

according to OGT’s patented methods if those arrays have either been purchased from

OGT’s licensed suppliers, or have been made by the customer under a license from OGT.

Please contact OGT to enquire about a license under OGT’s patents at

[email protected].

USE OF THIS INSTRUMENT WITH MICROARRAYS MAY REQUIRE A LICENSE FROM ONE OR

MORE THIRD PARTIES THAT HAVE PATENTS RELEVANT TO SUCH USE. MOLECULAR

DEVICES DOES NOT SUGGEST OR PROMOTE THE USE OF THIS INSTRUMENT IN A

MANNER THAT INFRINGES ON THE PATENT RIGHTS OF A THIRD PARTY. YOU ARE

ENCOURAGED TO EVALUATE WHETHER A LICENSE IS REQUIRED FOR YOUR SPECIFIC

APPLICATION OF THIS INSTRUMENT. COMPANIES THAT HAVE INTELLECTUAL PROPERTY

RIGHTS IN THE POTENTIAL FIELD OF APPLICATION OF THIS INSTRUMENT INCLUDE

WITHOUT LIMITATION, AFFYMETRIX, INC. (“AFFYMETRIX”), AGILENT, AND OXFORD

GENE TECHNOLOGY. THIS INSTRUMENT HAS NOT BEEN LICENSED OR APPROVED FOR

DIAGNOSTIC APPLICATIONS.

THE USE OF THIS INSTRUMENT IN CONNECTION WITH MICROARRAYS MAY BE WITHIN

THE SCOPE OF PATENTS HELD BY AFFYMETRIX. TO THE EXTENT THAT AFFYMETRIX

PATENT RIGHTS ENCOMPASS THIS INSTRUMENT OR ITS USE, AFFYMETRIX HAS

GRANTED A LIMITED PATENT LICENSE FOR RESEARCH USE ONLY AND NOT FOR USE IN

DIAGNOSTIC PROCEDURES. SUCHLICENSE, IF APPLICABLE, IS LIMITED TO USE OF THIS

INSTRUMENT WITH SPOTTED MICROARRAYS SEPARATELY LICENSED BY AFFYMETRIX.

NO LICENSE IS CONVEYED, BY IMPLICATION, ESTOPPEL OR OTHERWISE, TO USE THIS

INSTRUMENT WITH MICROARRAYS MADE USING IN SITU OR PHOTOLITHOGRAPHIC

SYNTHESIS. NO OTHER LICENSE IS CONVEYED, BY IMPLICATION, ESTOPPEL OR

OTHERWISE, UNDER ANY AFFYMETRIX PATENT OR OTHER INTELLECTUAL PROPERTY

RIGHT.

This instrument is licensed by Affymetrix under the following patents: U.S. Patent Nos.

5,578,832;5,631,734; 5,834,758; 5,936,324; 5,981,956; 6,025,601; 6,141,096;

6,171,793; 6,185,030; 6,201,639;6,207,960; 6,218,803; 6,225,625; 6,252,236;

6,262,838; 6,335,824; 6,403,320; 6,403,957, 6,407,858;6,472,671; 6,490,533;

6,545,264; 6,597,000; 6,643,015; and 6,650,411.

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Contents

Foreword . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Who This Manual Is For . . . . . . . . . . . . . . . . . . . . . . . . . 7

Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . 7

Chapter 1 Principles of Operation . . . . . . . . . . . . . . . . . . 9

Scanner Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Scanner Components . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Scanner Specifications . . . . . . . . . . . . . . . . . . . . . . . . . 11

Site Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Chapter 2 Installation and Operation . . . . . . . . . . . . . . 13

Unpacking the scanner and positioning it on the bench. . . 13

Installing the Software . . . . . . . . . . . . . . . . . . . . . . . . . 16

Turning on the Scanner . . . . . . . . . . . . . . . . . . . . . . . . 17

Inserting a Slide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Shutting Down the Scanner. . . . . . . . . . . . . . . . . . . . . . 19

Chapter 3 Maintenance & Troubleshooting . . . . . . . . . . 21

Moving the Scanner . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Interlock Failure Symptoms . . . . . . . . . . . . . . . . . . . . . 23

Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Appendix A Instrument Components. . . . . . . . . . . . . . . 25

Protective enclosure . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Optics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Lasers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Optical Path. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Emission Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

PMT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Status Lights . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Appendix B Instrument Performance Factors . . . . . . . . 29

Spatial Resolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Dynamic Range and Detection Limit . . . . . . . . . . . . . . . . 31

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Contents

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Appendix C Warranty and Service . . . . . . . . . . . . . . . . . 33

Standard Warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Out-of-Warranty Repair Service . . . . . . . . . . . . . . . . . . 33

Optional Service Agreement. . . . . . . . . . . . . . . . . . . . . 33

Technical Support. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

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Foreword

The foreword describes the intended audience for the manual. It

defines the typographical conventions used in the manual and lists the

Related Documentation

The customer documentation for the GenePix 4000B Microarray

Scanner includes the GenePix® Pro Software Reference Guide, Safety

Practices manual, and the GenePix® Pro online Help.

WARNING! A warning indicates an operation that can cause

personal injury if precautions are not followed.

Tip! Provides useful information that helps apply the techniques and

procedures in the text to your specific needs, and provides shortcuts,

but is not essential to the completion of a procedure.

Note: Provides essential information for the completion of a procedure.

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Foreword

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Principles of Operation

The GenePix® 4000B Microarray Scanner uses a laser-excitation based

fluorescence scanning and imaging system. The laser-based scanning

system operates by slowly moving the slide in the Y–direction, while

the slide is rapidly scanned in the X–direction. The design of the

scanner allows you to scan a 25 mm by 75 mm slide at up to two

wavelengths:

•10 μm resolution in approximately 6.5 minutes

•5 μm resolution in approximately 13 minutes

Scanner Features

•Two internally installed laser-excitation sources

•A user-attenuated lasers allowing 10%, 33%, and 100%

transmission

•Simultaneous scanning of two wavelengths

•User-adjustable focus

•Precisely controlled automatic laser power monitoring with

pixel-by-pixel correction

•Data Scan pixel resolution from 5 m to 100 μm

•Fast Preview Scan pixel resolution at 40 μm

•16-bit ultra-low-noise digitization

•Dynamic range of 104

•Two filters (670DF40 and 575DF35)

•Capacity for one standard 1 inch by 3 inch (25 mm by 75 mm,

or 26 mm by 76 mm) microscope slide-based microarray

•Full integration with GenePix Pro Software and Acuity®

Microarray Informatics Software

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Principles of Operation

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Scanner Components

The main components of the GenePix 4000B Microarray Scanner are:

•Protective enclosure

•Optics

•Lasers

•Optical path

•Emission filters

•PMTs (photo-multiplier tubes)

•Status lights

•External power supply

Figure 1-1 GenePix® 4000B Microarray Scanner

For detailed information about each component, see Instrument

Components on page 25.

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GenePix 4000B Microarray Scanner User Guide

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Scanner Specifications

Table 1-1 Specifications

Sample type Standard microscope slides (1 inch by 3 inches, 25

mm by 75 mm or 26 mm by 76 mm; 0.9 to 1.2 mm

thick)

Maximum scan area 22 mm by 72 mm

Maximum resolution 5 μm

Scan mode and order Simultaneous scanning of two wavelengths

Detector Dual PMTs

Signal digital output 16-bit

Image format Single or multi-image TIFF

Computer interface USB 2.0

Scan time 6.5 minutes at 10 μm resolution

Dynamic range Four orders of magnitude

Uniformity Plus or minus 10%

Dimensions 13 inches wide by 8.7 inches high by 17.4 inches long

(36 cm by 22 cm by 44 cm).

Weight 35.8 lb (16.2 kg)

Power supply Line voltage: 85 to 264 VAC (110 to 340 VDC)

universal voltage input

Line frequency 50 to 60 Hz

Power 85 W, Fuse: 2.0 A slow. 5 to 20 mm

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Principles of Operation

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Site Requirements

Table 1-2 Site Requirements

Temperature 50 to 86ºF (15 to 30ºC)

Humidity 5 to 95% non-condensing

Power Universal input 50 to 60 Hz, 100 to 240 VAC, 2A max

Space 25.6 inches deep by 16.9 inches wide by 13.4 inches high

(65 cm by 43 cm by 34 cm). An additional 6 inches (15.2

cm) for clearance.

Bench support Sufficient to support 40 lbs (18 kg) with minimal vibration

Uninterruptible

power supply

(UPS)

We recommend the use of a 325 VA UPS

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Installation and Operation

The GenePix® 4000B Microarray Scanner should be unpacked and in

position on a flat level surface before performing any of the installation

procedures. Perform the procedures in the following order.

•Unpack the scanner and position it on the bench

•Install the software

•Turn on the scanner

•Insert a slide

Unpacking the scanner and positioning it on the bench

The GenePix 4000B Microarray Scanner is packed in a specially

designed crate. Retain the crate and the packing materials. If the

scanner requires repair, you must return it in the original packaging. If

the crate has been damaged in transit, you must retain it for inspection

by the carrier.

WARNING! Shock Hazard. In an emergency, users must be

able to safely disconnect the main power cable without moving

the scanner. Locate the scanner so that either the power outlet

or the scanner’s appliance connector is accessible.

WARNING! The scanner weighs 35.8 pounds (16.2 kg). To

avoid potential injury, a minimum of two people are needed to

lift the scanner.

WARNING! Biohazardous Material. Do not operate the scanner

in an environment where potentially damaging liquids or gases

are present, or in a room with a temperature below 15°C.

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Installation and Operation

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To unpack the scanner and position it on the bench

1. Open the crate and remove any foam blocks used to protect the

scanner from excessive shock and vibration during shipping.

CAUTION! Do not touch or loosen any screws or parts other than those

specifically described in the instructions. Doing so can cause

misalignment and voids the scanner warranty.

2. Lift and then place the scanner on a flat level surface, away from

direct sunlight, dust, drafts, vibration, and moisture. Carefully

move the scanner to its final position.

3. Plug the USB cable into the USB type B port on the back of the

scanner, and the USB type A port on the control computer.

Note: Do not tilt or slide the scanner when transferring it from

the crate to its final position on a bench or desk.

Tip! For proper ventilation and cooling, leave at least six inches

of space between the back of the scanner and the nearest

object or surface.

Figure 2-1 Connections on back of the scanner

Item Name

1 Round port for main power supply cable

2 USB type B port

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GenePix 4000B Microarray Scanner User Guide

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4. Plug the round connector of the cable leading from the external

power supply into the matching power port on the back of the

scanner. Plug the main power supply cable into the external

power supply, and the lab’s power outlet.

We recommend you use a surge protector between the main

power cable and the power outlet.

Figure 2-2 Main power supply cable components

Item Name Description

1 Round connector Plug into the matching power port on

instrument’s back panel

2 External power supply

3 Main power cable Plug end 3a into the external power

supply. Plug end 3b into the lab’s

power outlet.

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Installation and Operation

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Installing the Software

Before operating the scanner, you must install the GenePix Pro

Software on a Windows-based control computer.

To install the software

1. Locate the GenePix Pro Software CD.

2. Read the supplied software installation instructions.

3. Insert the GenePix Pro Software CD into the computer. Follow

the InstallShield Wizard instructions to install the GenePix Pro

Software.

CAUTION! Do not to insert the security key into the control computer

until after the GenePix Pro Software has been installed.

4. Install the security key. For more information, see the GenePix®

Pro Software Reference Guide included with the GenePix Pro

Software.

Note: You must be fully aware of the information contained in

the GenePix® Pro Software Reference Guide to ensure a

successful software installation. The installation instructions are

provided in hard copy, and soft copy on the GenePix Pro

Software CD.

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GenePix 4000B Microarray Scanner User Guide

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Turning on the Scanner

Proper startup of the GenePix 4000B Microarray Scanner includes a

functional checkout procedure to confirm that the scanner is performing

according to the specifications established during commissioning before

the scanner left the factory.

To turn on the scanner

1. Make sure the slide door is closed.

2. Turn on the scanner power switch.

3. Turn on the control computer.

4. Click Start > Programs > Molecular Devices > GenePix

Pro, and then click the Report tab.

5. Click Functional Checkout in the Hardware Diagnostics

Reports area, and follow the steps in the Wizard.

The GenePix Pro Software automatically logs hardware

performance events into the Hardware Diagnostics Report every

two hours during operation.

Inserting a Slide

The slide holder is a precision component designed to ensure proper

focusing and field uniformity. Improper handling can damage the slide

holder and affect imaging performance.

CAUTION! Never touch the slide holder while it is moving. Never force

the slide holder closed, or apply significant pressure to it.

To insert a slide

1. Move the slide door to the left.

The slide holder moves forward into the load position.

2. Raise the top of the slider holder.

Tip! The GenePix 4000B Microarray Scanner power switch is

located on the instrument’s external power supply module.

Note: For optimum performance, allow the GenePix 4000B

Microarray Scanner to warm up for 15 minutes before scanning

slides with the GenePix Pro Software.

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Installation and Operation

18 5000450 D

3. With the slide held between your thumb and finger, carefully

place the slide, feature-side down into the slide holder.

4. Lower the top of the slide holder.

Note: Make sure the barcode on the slide is facing the

front of the scanner.

Figure 2-3 Slider holder

Ite

mName Description

1 Slide door In open position

2 Slide holder In load position

3 Slide Place feature-side down

4 Barcode Barcode is facing the front of the scanner

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GenePix 4000B Microarray Scanner User Guide

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CAUTION! Make sure the top of the slide holder is lowered before

closing the slide door.

5. Move the slide door to the right.

The slide holder moves into the scan position.

Shutting Down the Scanner

Proper shutdown of the GenePix 4000B Microarray Scanner ensures the

scanner or software are not damaged.

To shut down the scanner

1. Close the GenePix Pro Software.

2. Turn off the scanner power switch.

3. Turn off the control computer.

Tip! The GenePix 4000B Microarray Scanner power switch is

located on the instrument’s external power supply module.

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Installation and Operation

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Molecular Devices GenePix 4000B User manual

Brand: Molecular Devices

Model: GenePix 4000B

Type: User manual

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Molecular Devices GenePix 4000B User manual

Molecular Devices GenePix 4000B User manual

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